Anthony Hopkins Schools Charlie Rose on the Religion in Science

As if we needed more evidence that myths abound regarding how science handles religion, Charlie Rose supplied it in abundance in his interview with legendary actor Anthony Hopkins last week. Fortunately Hopkins was able to disabuse the audience of Rose’s misconceptions, though it is not clear Rose was the better for it. Here is the relevant discussion, beginning at the 11:25 mark of the interview:

CR: You see it’s fascinating to me, because I’ve had, in a variety of television series—things that I have done having to do with scientists—and scientists can’t go there, because they can’t prove it—

AH: Can’t go where?

CR: To faith! Because they’re not willing to—most of them, certainly there are exceptions—but I mean people like, you know Nobel Laureates. They can’t go there, because they can’t prove it … Scientists in the end say “I can’t go there,” because they can’t prove it, and their intellectual—their whole being as a scientist—

AH: But there are many physicists who do believe. Dealing in particle physics for example, people are getting close to the essence of power of the—

CR: Well that’s part of what they’re working on in Geneva, is sort of the duplicating creation—

AH: And Einstein said … I don’t believe in a personal god, I believe in the god of Spinoza, where there’s an intelligence and a supreme awe-inspiring design at the back of the cosmos, starting from the Big Bang. Charles Darwin was a staunch member of his own church—he was a protestant. And when he went on the voyage of the Beagle it astonished him, the extraordinary range of life, and the power of life itself. And he never gave up his faith. Galileo was a man of the church—never opposed the church, but he got into a lot of trouble because he said things that upset the apple cart.

Hilarious. In response to Rose’s mythical meanderings, the actor Anthony Hopkins, without a moment of preparation, launches into a perfectly cogent discussion of the relationship between science and religion. In the space of 1 minute and 16 seconds Hopkins effectively deconstructs the media’s mythology. He begins with the diagnosis, cutting to the core with the simple question: “Can’t go where?” From there he begins with today’s scientists, and then progresses through classic historical examples (in order!) of Einstein, Darwin and Galileo—three of the most influential scientists in the history of modern science, each with their own different faith. Yes, his description of Darwin’s faith commitment may have been slightly off, but his overall thesis was spot on. I’m sure the audience learned something, but I doubt the myth makers did.

The Enduring Warfare Thesis Theses

Though historians tell us that the warfare thesis—the idea that the relationship between science and religion has been mostly one of conflict—is discredited, there seems to be a great many who have not yet learned of its demise. Not only is the warfare thesis alive and well in popular culture, it is also promoted by those who probably should know better. In fact in the origins debate each side has its own version. Why is the warfare thesis so enduring? One reason is that, like any good lie, there is some truth to it. Probably a better reason is its rhetorical power. But perhaps the main reason is that we need it—our religion demands it.

The warfare thesis is usually identified with a nineteenth century evolutionary movement that cast evolution skepticism as religiously driven. Men such as Darwin confidant Thomas Huxley, chemistry professor John Draper and Cornell University cofounder Andrew White promoted the warfare thesis as a general trend in the relationship between religion and science.

A popular prooftext is the Galileo Affair. But the seventeenth century debate about geocentrism versus heliocentrism, involving Galileo and the Roman Catholic Church, was hardly obvious. Subtleties in both the science and religion make simple stereotypes difficult to come by. Rather than serving as supporting evidence, the Galileo Affair is one of many problems with the warfare thesis.

Of course there are people who oppose strong scientific findings on religious grounds. Geocentrism still has its proponents. But the relationship between science and religion has generally been far more complex than one of simple obstructionism and conflict.

What the warfare thesis did provide, nonetheless, was powerful evolutionary rhetoric. This is exemplified no better than in Jerome Lawrence’s and Robert Lee’s Inherit the Wind. I once debated an evolutionist professor directly following the staging of this fictionalized account of the 1925 Scopes Monkey trial. It was like arguing against a war after a propaganda film. I made some powerful scientific points but they were met with empty stares while the professor’s metaphysical mandates for evolution received approving nods all around.

It was yet another example of the complexity of the relationship between science and religion. I, though billed as the “science skeptic,” made scientific arguments whereas the professor, though billed as the “science defender,” made religious arguments.

Historians note that religion has provided ideas for science. Did not Darwin learn about scarce resources from the cleric Thomas Malthus? But evolutionary thought does not merely draw on a few religious ideas for inspiration. Evolution rests on a religious foundation and mandate that dates back long before Darwin and remains crucial today.

In evolutionary thought, the relationship between science and religion is better modeled according to the centuries old adage: Theology is queen of the sciences. This view, of course, badly damages evolution’s claim to be a scientific fact and hence the warfare thesis. How better to handle a liability than to assign it to the opposition? Evolutionists need the warfare thesis, their religion demands it.

The other warfare thesis

But evolutionists are not the only ones who have a warfare thesis. Evolution’s skeptics also have one. While evolutionists blame the skeptics for being religious, the skeptics blame evolutionists for not being religious. Consider the seventeenth century Anglican cleric Thomas Burnet who was accused of atheism by Richard Bentley. Burnet was widely read and had lasting influence. He presented a variety of evidences and arguments that god would only use natural laws and processes to create the world. One may agree or disagree with his ideas, but Burnet certainly was no atheist.

A century later the equally religious James Hutton endured the atheist accusation, and after Darwin it became common for skeptics to equate evolution with atheism or naturalism. Most recently Albert Mohler writes:

The debate over Darwinism rages on, with almost every week bringing a new salvo in the great controversy. The reason for this is simple and straightforward – naturalistic evolution is the great intellectual rival to Christianity in the Western world. It is the creation myth of the secular elites and their intellectual weapon of choice in public debate.

In some sense, this has been true ever since Darwin.  …

Darwin’s central defenders today oppose even the idea known as “Intelligent Design.” Their worldview is that of a sterile box filled only with naturalistic precepts.

From the beginning of this conflict, there have been those who have attempted some form of accommodation with Darwinism. In its most common form, this amounts to some version of “theistic evolution” – the idea that the evolutionary process is guided by God in order to accomplish His divine purposes.

But evolutionary thought does not stem from naturalistic precepts. True, evolutionists insist on strict secondary causation in their explanation of origins, but the motivation and justification for this dogma is religious. And just as the evolutionary warfare thesis holds scientific concerns to be inconsequential compared to the supposed religious motivations, so too this warfare thesis holds religious arguments to be inconsequential compared to the supposed atheism or materialism. Such religious arguments are, according to this warfare thesis, nothing but mere accommodationism.

As before, there is much truth to this thesis. Certainly evolution has fueled atheism and materialism. And the growing atheism, in turn, promotes evolution. But evolution also fuels theism. Process theology, for instance, has strong influences from evolution. This is hardly surprising given the religious thought that mandated evolution in the first place. Any atheism to be found is parasitic on the underlying theism. Far from an attempt at accommodation, the theism is the driving force.

Consider, for example, the case of eighteenth century religious skeptic, David Hume. The influential Scottish philosopher promoted evolutionary thought and Darwin was well versed in Hume’s arguments which occasionally even show up in Origins, albeit with the usual Darwinian touch of subtlety.

If ever there was an opportunity to trace the path of atheism’s or naturalism’s influence it would be here. But what we find is exactly the opposite. Hume’s (and Darwin’s) arguments were mostly theological and occasionally philosophical, but never from atheism. Indeed, while Hume was a great rhetoritician and creative in his own right, many of his arguments can be seen in earlier theists.

It is not a large step to move from Malebranche’s and Leibniz’s naturalistic solutions to the problem of evil to Hume’s argument against a divine design of a world so filled with misery. And like any good student of debate, Hume could with equal skill marshal the opposing arguments. Arnauld’s rejection of such theodicies by appeal to the mysteries of the divine can be seen in Hume’s anthropomorphic warning. We must not think we can anywise conceive the perfections of god, so the design inference must be rejected. And Hume’s arguments against miracles came after decades of debate amongst theists.

Hume is by no means an isolated example. Today, for instance, Richard Dawkins argues god would never have designed the blind spot in our retina, and PZ Myers believes god would not have created this universe. And more important than the atheists are the theists who initiated and promoted the many metaphysical arguments that mandate evolution. For centuries they have insisted god would work strictly through secondary causes and be undetectable. This is the foundation of evolutionary thought. It is anything but atheistic.

But while this warfare thesis may not be accurate, it is powerful rhetoric. How better to construct an enemy than to blame it on the secularists or atheists? As with the evolutionist’s warfare thesis, this one is an enduring theme.

And by blaming evolution on the atheists one can avoid the difficult metaphysical and theological issues evolutionists raise. What about Burnet’s and Kant’s greater god argument, and what about Leibniz’s problem of evil? And what about those fossils and design similarities? There is no need to address these evolutionary questions if it can all be dismissed as a secularist agenda. But it isn’t.

In the origins debate each side has its own warfare thesis, and these opposing theses serve many purposes. Unfortunately these theses are misconceptions at best, and self-serving religiously driven fictions at worst.

Insect Eyes Inspire More Efficient Solar Power

Moths not only see well in the night, they also keep a low profile and that technology is now making its way into solar cell design. As one report explains:

The eyes of moths, which allow them to see well at night, are also covered with a water-repellent, antireflective coating that makes their eyes among the least reflective surfaces in nature and helps them hide from predators in the dark. Mimicking the moth eye's microstructure, a team of researchers in Japan has created a new film, suitable for mass-production, for covering solar cells that can cut down on the amount of reflected light and help capture more power from the sun.

It is yet another example of nature’s remarkable designs finding application in engineering work.

The Hierarchy of Evolutionary Apologetics: Protein Evolution Case Study

A common retort from evolution’s defenders is that all those scientists can’t be wrong. Is it conceivable that so many scientific papers and reports, with their conclusions about evolution, are making the same mistake? Before answering this we first must understand the hierarchy of the evolution apologetics literature. At the base of the pyramid are the scientific papers documenting new research findings. Next up are the review papers that organize and summarize the state of the research. And finally there is the popular literature, such as newspaper and magazine articles, and books. Across this hierarchy evolutionists make different types of claims that should not be blindly lumped together. Yes, there are problems across the spectrum, but they tend to be different kinds of problems.

Background: The Hierarchy of Evolutionary Apologetics

Scientific papers document important and perfectly legitimate research. The results are usually presented carefully and rarely are they exaggerated. And it is difficult to find such papers claiming that evolution is a fact.

These papers do, however, discuss the results strictly in terms of evolution. No matter how unlikely evolution is given the results, they are interpreted as though evolution were the only explanation. Problematic results, and they are common, are not allowed to suggest epistemological challenges. They may only pose theoretical problems.

The authors cannot suggest that we may not, after all, know evolution to be a fact. They may only point out our ignorance of how it is supposed to have occurred. In all of this it is difficult to avoid misrepresentations of the research results, but such blunders are limited by the narrow scope of such papers.

Review and survey papers, on the other hand, do make more expansive evolutionary claims. These review papers draw on the vast body of research literature to organize and summarize the state of the research. They draw broader conclusions, and when discussing the subject of evolution these papers are more likely to make obviously unsupportable evolutionary claims.

Finally the popular literature is the next step beyond the review papers. If the review papers are summaries for scientists, the popular literature provides summaries for the non scientific audience. It is here that the dogmatic, sweeping evolutionary claims are most prevalent. Evolution must be a fact, all the scientific evidence unquestionably supports and proves evolution, doubters have nothing but nefarious motivations, there is war between science and religion, and so forth.

In terms of sheer magnitude, the first category—the narrowly focused research papers—dominates the literature. And here there is far less speculation and far more technical detail. Problems do arise in the evolutionary interpretations of the results, but such speculation is a minor part of the paper.

But like toxic pollutants that accumulate and reach increasing concentrations at higher levels of the food chain, the speculation becomes amplified in the review papers, and then even more so in the popular literature. Like a morphing rumor, what begins as tentative and unlikely speculation of how evolution might account for problematic findings ultimately becomes yet another evolutionary proof text in the popular literature.

So when evolutionists argue that those scientific papers and reports cannot all be wrong, we might agree with them. The technical details of the scientific research are certainly not wrong. True, there are misrepresentations of science when the results are force fit into evolution, but the far more egregious misrepresentations of science are found as one moves up the hierarchy of the evolution literature.

Case study: Protein evolution

Imagine a choppy ocean filled with waves for as far as the eye can see. Meanwhile the sky is dotted with an occasional jet airliner flying far above. This scene gives an idea of what science is telling us about protein evolution. A protein consists of hundreds of amino acids glued together in a long sequence. Because nature uses 20 different amino acids, the total number of possible sequences is astronomically huge. For a protein with 300 amino acids in all, for instance, there are 20^300 (roughly equal to a one followed by 390 zeros) different possible sequences.

It is an ocean of possibilities. But the vast majority of these possible amino acid sequences are worthless to evolution. Not only are they essentially dysfunctional themselves, but even as evolutionary starting points they don’t lead to much better designs. If you evolve a typical randomly selected amino acid sequence, you can improve the design a bit, but the search quickly stagnates.

Like the choppy ocean, the protein function landscape seems to be filled with a great many swells. Evolution can move up from the bottom of a swell to the top of a nearby wave, but this is only a minor improvement in the protein function. Go any further and evolution would fall into the neighboring swell, leaving it no better off than when it started.

Very rarely, in this seemingly endless sea of minor ups and downs, an extremely efficient, functional protein punctuates the protein function landscape. Here the landscape rapidly shoots up into the sky. This is not a gradual rise leading to these lofty and tiny regions of functional proteins. Rather, the landscape abruptly rises to heights far above the ocean’s surface. Like the jet airliners flying far above the ocean, proteins appear to be rare events in an otherwise non descript landscape.

Several types of protein studies point to this conclusion. Some of these studies begin with random amino acid sequences and attempt to evolve them toward nature’s proteins or something like them. These studies show that only minor functionality can be evolved from random starting points. Nature’s marvels, or anything like them, are so astronomically rare evolution would never find them using its blind, adaptive walk. (This is to say nothing of how the machinery for such a search could have evolved in the first place.)

Other studies begin not with a random amino acid sequence, but rather work backwards from a known protein. These studies show that proteins are quite sensitive. The function of a typical protein exponentially degrades as random mutations are introduced.

Whether we start at the beginning or the end, the science tells us that the protein function landscape is not one of smooth funnels leading to fantastic molecular machines, as evolution would expect.

And as it seems to be with so much of biology, when scientists work with nature’s designs some fascinating engineering can be done. Just as the design of a jet aircraft can be adjusted and augmented to meet a new performance requirement, so too proteins can be adapted to meet desired properties. And just as engines or other components can sometimes be swapped between aircraft, so too proteins are marvelously modular, allowing for new designs to be created by mixing and matching.

Unfortunately evolutionists routinely conflate such design engineering with evolutionary possibilities. Proteins are adaptable, so can’t they gradually evolve? Proteins are module, so can’t they just swap designs when gradualism fails? The science contradicts such conclusions, but evolutionists are driven more by their theory than by the data. Here are two examples.

An example research paper

In this research paper, evolutionists investigated how proteins might have evolved. They attempted to demonstrate the evolution of a virus—a molecular machine consisting of several proteins—in the laboratory. To simplify the problem they started with all but a small part of the virus intact. They randomized the amino acid sequence of one part of one of the viral proteins, and they repeatedly evolved that randomized segment in hopes of reconstructing the entire virus.

What they discovered was that the evolutionary process could produce only tiny levels of functionality (in this case the virus’ ability to infect a host). Their evolved sequences showed no similarity to the native sequence which is supposed to have evolved. And the best virus they could produce, even with the vast majority of the virus already intact, was several orders of magnitude weaker than nature’s virus.

The reason their evolutionary process failed was that the search for better amino acid sequences, that would improve the virus’ ability to infect the host, became too difficult. A possible evolutionary explanation for these disappointing results is that in such a limited laboratory study, the evolutionists were simply unable to reproduce what the vast resources of nature could produce. Perhaps in the course of time evolution could evolve what the evolutionists could not do in the laboratory.

But the results refuted even this fall back explanation. In fact, the evolutionists would not merely need an expanded study with more time in the laboratory, they would need more time than evolution ever had—many times over. The number of experiments they would need to conduct in order to have any hope of evolving a virus that rivals nature’s version is difficult to compute. But it is at least 10^70 (a one followed by 70 zeros).

And yet, there it is. This relatively short sequence of amino acids exists as part of of the virus, with its fantastically high infection capabilities. And of course this is not merely a problem for a part of one protein, in one virus. It is a problem for all life, for proteins are crucial molecular machines throughout biology.

But not surprisingly the evolutionists interpreted their results according to their theory. The majority of the paper presents the detailed scientific results. There is no misinterpretation or exaggeration, until that is, the discussion of the implications for evolution. The evolutionists write:

Such a huge search is impractical and implies that evolution of the wild-type phage must have involved not only random substitutions but also other mechanisms, such as homologous recombination.

Homologous recombination? It would be difficult to imagine a more unlikely explanation. Homologous recombination is a complex genetic mechanism assisted by finely-tuned proteins. It is circular to recruit such a mechanism for the initial evolution of proteins—for no such mechanism is likely to have existed. And that is putting it mildly.

And even if homologous recombination could somehow have been in play, it wouldn’t help anyway. For while this is a clever mechanism for the swapping of nature’s protein modules, it does not help when used with sequences that are nowhere close to solving the problem. Jumping from one ocean wave to another doesn’t improve the odds in finding the astronomical, one-in-10^70, longshot.

The evolutionists found that it is impossible for evolution’s gradual search to solve the problem, even for the single module they were experimenting with (and all the other modules in the virus already at their native sequences). But if repeated attempts by evolution are going to fail, then the mixing and matching of those errant attempts will not help either. They merely represent another blind attempt. Unfortunately, it is unscientific conclusions such as these that inform the next level up in the apologetics hierarchy.

An example survey paper

This survey paper is entitled “Exploring protein fitness landscapes by directed evolution.” The paper discusses both the engineering problem of creating new proteins and its implications for how proteins evolved in the first place. For the most part this survey paper is a helpful and accurate summary of the relevant scientific findings at the time. The enormous complexity of the problem, and even the challenges for evolution are clearly stated. Here are several examples from the paper:

Notwithstanding significant advances, a molecular-level understanding of why one protein performs a certain task better than another remains elusive. This state of affairs is perhaps not surprising when we remember that a protein often undergoes conformational changes during function and exists as a dynamic ensemble of conformers that are only slightly more stable than their unfolded and nonfunctional states and that might themselves be functionally diverse. Mutations far from active sites can influence protein function. Engineering enzymatic activity is particularly difficult, because very small changes in structure or chemical properties can have very significant effects on catalysis. Thus predicting the amino acid sequence, or changes to an amino acid sequence, that would generate a specific behavior remains a challenge, particularly for applications requiring high performance (such as an industrial enzyme or a therapeutic protein). Unfortunately, where function is concerned, details matter, and we just don't understand the details. …

Although the distance between any two sequences is small (that is, equals the number of mutations required to interconvert them and is therefore ≤ L), this high-dimensional space contains an incomprehensibly large number of possible proteins. For even a small protein of 100 amino acids there are 20^100 (~10^130) possible sequences, or more than the number of atoms in the universe. Searching in this space for billions of years for solutions to survival, nature has explored only an infinitesimal fraction of the possible proteins. …

The vast size of sequence space makes it impossible to characterize (or even model) more than a minute fraction of this fitness surface. Despite this, several important features have emerged from accumulated experimental studies. The first is the low overall density of functional sequences: the vast majority do not code for any functional protein, much less the desired protein. …

Because most mutations are deleterious, the probability that a variant retains its fold and function declines exponentially with the number of random substitutions, and random jumps in sequence space uncover mostly inactive proteins. Thus new functions are extremely difficult to obtain without altering some aspect of the search. One approach is to create a new starting point, a parent protein with at least some minimal function, and improve that by directed evolution. …

An approach to making multiple mutations that is used extensively in nature is recombination. Naturally-occurring homologous proteins can be recombined to create genetic diversity within protein sequence libraries. …

Furthermore, natural evolution works on a different fitness landscape, and it is unclear how the protein fitness assayed during directed evolution is related to the organismal fitness that natural evolution optimizes.

These passages discuss some of the difficulties in using protein engineering as evidence for evolution, and some of the contradictory evidence protein engineering has produced. Unfortunately, none of this is interpreted outside of the evolutionary framework, and in fact the paper goes well beyond, and against, the scientific data in elaborating the evolutionary narrative:

Millions of years of life's struggle for survival in different environments have led proteins to provide diverse, creative and efficient solutions to a wide range of problems, from extracting energy from the environment to repairing and replicating their own code. …

Evolution, however, had no difficulty generating these impressive molecules. …

Evolution is unique because it works at all scales, from molecules to ecosystems — no other engineering design algorithm can make that claim. A simple algorithm of mutation and artificial selection has proved effective for everything from the selective breeding of plants and animals to discovering self-replicating nucleic acid sequences. …

Among the large number of mutational trajectories between a starting point and a solution, smooth uphill paths can often be found. …

Despite the vast size of sequence space and the complex nature of protein function, the Darwinian algorithm of mutation and selection provides a powerful method to generate proteins with altered functions.

This is the apologetics message of the paper that informs the popular literature. Whereas the research paper’s undefendable, non scientific statements were limited, now in the survey paper they frame the narrative from beginning to end. Evolution, one way or another, must have happened, so the evidence must support it. There can be no contradictory evidence.

To make this story sound scientific, the paper equivocates on evolution. It conflates the protein engineering findings that nature’s proteins can adapt with the evolutionary narrative:

Despite their complexity and finely-tuned nature, proteins are remarkably evolvable: they can adapt under the pressure of selection, changing behavior, function and even fold. …

Biological components and systems have shown a remarkable ability to adapt under the pressure of artificial selection, an evolvability that very likely reflects their own history of natural selection. …

Even the earliest directed evolution experiments noted how rapidly proteins could adapt to new selective pressures, indicating the ready availability of smooth uphill paths in the fitness landscapes. …

This simple uphill walk on a fitness landscape in sequence space works because proteins are wonderfully evolvable and can adapt to new conditions or even take on new functions with only a few mutations.

Proteins are remarkably evolvable along smooth uphill paths because, after all, their adaptation under artificial selection reflects their own history of natural selection? Of course the adaptation of native proteins proves no such thing. It is yet another rehearsing of Darwin’s flawed logic that animal husbandry and breeding provide a peek into the mechanisms of change that, by the way, created all of biology. Religion drives science and it matters.

New Genes: Putting the Theory Before the Evidence

Imagine that you have been falsely accused of a crime. The police department has identified you as the prime suspect and they are busy gathering as much evidence against you as possible. They have constructed a theory of your motivations and actions, and as they gather the evidence they interpret it according to their theory. Their process of working from a preconceived notion of your guilt leads the police investigators to explain even ambiguous or contradictory evidence in ways that support their theory. And so it is the theory that is informing the evidence, rather than the evidence informing the theory. As crazy as it sounds, this approach is standard for evolutionists and here are three recent examples dealing with protein evolution.

Example 1: Evolving a virus

In this study evolutionists investigated how proteins might have evolved. They attempted to demonstrate the evolution of a virus—a molecular machine consisting of several proteins—in the laboratory. To simplify the problem they started with all but a small part of the virus intact. They randomized the amino acid sequence of one part of one of the viral proteins, and they repeatedly evolved that randomized segment in hopes of reconstructing the entire virus.

What they discovered was that the evolutionary process could produce only tiny improvements to the virus’ ability to infect a host. Their evolved sequences showed no similarity to the native sequence which is supposed to have evolved. And the best virus they could produce, even with the vast majority of the virus already intact, was several orders of magnitude weaker than nature’s virus.

The reason their evolutionary process failed was that the search for better amino acid sequences, that would improve the virus’ ability to infect the host, became too difficult. A possible evolutionary explanation for these disappointing results is that in such a limited laboratory study, the evolutionists were simply unable to reproduce what the vast resources of nature could produce. Perhaps in the course of time evolution could evolve what the evolutionists could not do in the laboratory.

But the results refuted even this fall back explanation. In fact, the evolutionists would not merely need an expanded study with more time in the laboratory, they would need more time than evolution ever had—many times over. The number of experiments they would need to conduct in order to have any hope of evolving a virus that rivals nature’s version is difficult to compute. But it is at least 10^70 (a one followed by 70 zeros).

And yet, there it is. This relatively short sequence of amino acids exists as part of of the virus, with its fantastically high infection capabilities. And of course this is not merely a problem for a part of one protein, in one virus. It is a problem for all life, for proteins are crucial molecular machines throughout biology.

Did the evolutionists conclude that proteins did not evolve? Did they suggest their findings are a problem for evolution? Did they even do so little as discuss the possibility that this one particular protein they studied may not have evolved?

No. There is not even a hint from the evolutionists there is a problem. In fact, the results are, in typical fashion, interpreted according to evolution. As usual, the evolutionists simply explained that evolution must have, somehow, solved the problem:

Such a huge search is impractical and implies that evolution of the wild-type phage must have involved not only random substitutions but also other mechanisms, such as homologous recombination.

But other mechanisms, such as homologous recombination, do not help. Homologous recombination, or any other mechanism that evolutionists can imagine, does not provide some ingenious end around the problem. Evolution cannot somehow brilliantly find the one in 10^70 long shot. The evolutionists rosy report is not data-driven, but theory-driven.

Example 2: Evolving a simple function

In this study evolutionists attempted to evolve a protein that binds to a simple, common chemical group. This function is so simple even random polypeptides sometimes have slight binding affinities. Using their laboratory process the evolutionists were able to evolve minor improvements to a random polypeptide’s binding affinity. But these small binding levels are hardly detectable. So not only is the function trivial (in order to improve fitness a protein needs to do more than merely bind to a chemical), but the levels observed are likely too small to make a difference anyway.

As with Example 1 the evolved amino acid sequences showed no similarity to nature’s sequences and when the evolutionists tried using a larger number of trials there was no sign of improved results.

Despite these feeble results the evolutionists made remarkable conclusions:

The ease of the functional development within a small sequence variety implies that enzyme evolution is prompted even within a small population of random polypeptides. … These results mark the implementation of Darwinian evolution in the system.

There is no comparison between the evolution of an enzyme and their polypeptides with minor binding affinities. And there certainly was no Darwinian evolution demonstrated in their results, for such evolution requires tangible fitness improvements which can be selected. It was good research work, but the interpretation was according to evolution.

Example 3: New genes

This example deals with new genes. When a gene is found in a large number of species, evolutionists assume it came from the common ancestor of those species, which would date far back into evolutionary history. But when a gene is found in only one or a few species, evolutionists must conclude it arose in the common ancestor of only those few species, and therefore more recently.

But how can a new gene arise so quickly? Genes that code for proteins are difficult to evolve in any case (see here and here), but the problem is accentuated when the time frame is shortened.

How a gene could have evolved is not the only problem with new genes. Such new genes, however they were supposed to have evolved, were expected to be less important. But in this study evolutionists noticed this wasn’t so.

The evolutionists compared what they assume to be new and old genes, and found no statistical difference in the importance of their functions. Knockout a new gene, and you are just as likely to kill the organism as when you knockout an old gene. In fact, the proportion of genes that are essential is similar in every assumed evolutionary age group they examined.

But once again, evolutionists do not hesitate in fitting awkward results into their framework. “These data,” the evolutionists deftly concluded, “suggest that new genes frequently and rapidly evolve essential functions and participate in development.”

In fact, outside of evolutionary theory, there is no reason to think these genes are any newer than other genes. And inside of evolutionary theory there is no scientific explanation of how proteins arise in the first place. Evolutionists are hardly in a position to assert that these data, or any other data for that matter, suggest new genes frequently and rapidly evolve, period. With little more than a bare assertion the evolutionists convert yet another unexpected finding into an evolutionary proclamation.

Evolutionists are bound to the preconceived notion that evolution must be a fact. It drives their thinking in spite of the scientific evidence, and they interpret any and all evidence in this light. It may sound crazy, but it is the theory that informs the evidence, rather than the evidence that informs the theory.

Protein Evolution: A Problem That Defies Description

Charles Darwin’s theory of evolution is scientifically unlikely. The idea that all of biology just happened to arise spontaneously over long time periods (yes, that is what the theory of evolution says) is not motivated by the scientific evidence. This can be seen at all levels of biology including, more prominently in recent years, at the molecular level. A good example of this is the scientific evidence on proteins, and what it says about evolution.

It is not that the scientific evidence reveals proteins to be particularly unlikely on evolution. Proteins are not known to be any less likely to have evolved than, say, DNA repair mechanisms, cellular signal transduction, the electron transport chain, neurons, cardiovascular systems, mice or blue whales. But proteins are a bit more amenable to analysis. As mysterious and difficult as proteins are, molecular biology can at least provide some data on their supposed evolution. In the digital molecular world experiments can show how profoundly evolutionary expectations have failed, and how much more faith required to continue with the theory.

One way to understand how unlikely is protein evolution is in their sensitivity to change. Proteins generally do not tolerate much change to their design. Their designs can vary, but not much. In the vast universe of all possible protein designs, they are not vast oceans but more like the tiny holes in a golf course. This evidence indicates the evolutionary process is unlikely to find them.

Another way to understand protein evolution is to start at the beginning rather than the end. That is, rather than analyzing nature’s proteins, one can start with a non functional, random chain of amino acids to see how easily it can migrate toward functional proteins via evolution’s processes of natural selection or drift. These experiments confirm that the evolution of a protein is scientifically unlikely.

Such experiments reveal what seemed rather obvious from biochemistry: evolutionary schemes are not likely to find the highly complex protein designs we find in nature. The results of such experiments fall short of anything close to the real thing. The resulting sequences of amino acids look nothing like what we find in nature, and the resulting functions are orders of magnitude short of what real proteins do.

In fact, such experiments typically need all kind of advantages to show much progress. For instance, some experiments only attempt to evolve a part of a protein, while the rest of the protein is already at nature’s design at the beginning of the experiment. And some experiments apply artificial selection on low levels of trivial functions which otherwise would not improve fitness at the organismal level.

But even with these advantages the results demonstrate the failure of evolutionary expectations. Unfortunately, evolutionists are less than forthright in their representation of what science is telling us. For example, here is how one journal paper reported its results:

By extrapolation, we estimated that adaptive walking requires a library size of 10^70 [a one followed by 70 zeros] with 35 substitutions to reach comparable fitness. Such a huge search is impractical and implies that evolution of the wild-type phage must have involved not only random substitutions but also other mechanisms, such as homologous recombination.

Here the evolutionists must admit the obvious, that the envisioned protein evolution via gradual changes and natural selection does not work. In fact it is ridiculously unrealistic. But they then deny the gravity of the problem. With nothing but speculation they resolve their astronomical long shot with “other mechanisms” such as homologous recombination.

It is one of the great tragedies of our time that most people lack the scientific training to appreciate the incredible absurdity of evolutionary thought. The suggestion that homologous recombination could resolve this astronomical long shot is the height of absurdity. This is not hyperbole.

What cannot be solved with a library size of 10^70 is not magically going to be resolved with homologous recombination. And this is not to mention that homologous recombination would not have even existed when proteins first evolved. Indeed, an army of specialized proteins is required before homologous recombination is even possible. If homologous recombination was the key to evolving proteins, then aircraft carriers were the key to winning the battle of Trafalgar.

Indeed, it is a difficult task to describe the immense magnitude of this evolutionary folly. Here’s my attempt: It would be like throwing a paper airplane from the top of a skyscraper and explaining that it will make a hole-in-one at a golf course on the other side of town. On second thought, that still does not do the job—the evolutionary folly is far greater than this.